Mitochondrial ATP synthase is an F-type ATPase. It catalyses the formation of ATP and Pi accompanied to the flow of protons from the P to N side of the membrane. ATP synthase also called complex V has two distinct components:

F₁ – a peripheral membrane protein

F₀ – integral to the membrane, and 0 stands for oligomycin sensitive

Efraim Racker first identified this enzyme.

F₁ has nine subunits of five different types, with the composition α₃β₃γδε. Each of the three β subunits has one catalytic site for ATP synthesis. John E Walker determined the F₁ structure.

The knob-like portion of F₁ consists of alternating α and β subunits arranged like sections of an orange.

The polypeptide that makes up the stalk in the F₁ crystal structure is asymmetrically arranged with one domain of the single γ subunit, making up a central shaft that passes through F₁ and another domain of γ associated primarily with one of the three β subunits.

The F₀ complex, making up the proton pore, is composed of three subunits. a, b, and c in the proportion ab₂c₁₀. Subunit c is a small very hydrophobic polypeptide, consisting almost entirely of two transmembrane helices with a small loop extending from the matrix side of the membrane. The γ ε subunits of F₁ form a leg and foot that project from the bottom side of F₁ and stand as firm rings of (subunits as shown in Figure 8.21).

Figure 8.21 Structure of ATP synthase